Use of an interface contact statistics to rescore protein-protein docked ensembles
Abstract:
The recently developed statistical measure for the type of residue-residue contact
at protein complex interfaces, based on a parameter-free definition of contact,
has been used to define a contact score that is correlated with the
likelihood of correctness of a proposed complex structure.
Comparing the proposed contact scores on the native structure
and on a set of model structures the proposed measure was shown to
generally favor the native structure but in itself
was not able to reliably score the native structure to be the best.
Adjusting the scores of redocking experiments with the contact score showed
that the adjusted score was able to move up the ranking of the
native-like structure among the proposed complexes when the native-like
was not ranked the best by the respective program.
Tests on docking of unbound proteins compared the contact scores
of the complexes with the contact score of the crystal structure
again showing the tendency of the contact score
to favor native-like conformations.
The possibility of using the contact score to improve the
determination of biological dimers in a crystal structure was also explored.